Bull. Natl. Mus. Nat. Sci., Ser. B, 43(2), pp. 33–44, May 22, 2017 DNA Extraction, PCR and Sequencing were largely Unsuccessful from the Type Specimens of Mushrooms but Some 50-year-old or Older Specimens produced Authentic Sequences Kentaro Hosaka Department of Botany, National Museum of Nature and Science, Amakubo 4–1–1, Tsukuba, Ibaraki 305–0005, Japan E-mail: [email protected](Received 16 March 2017; accepted 22 March 2017) Abstract DNA extraction, PCR and sequencing of the nuclear ribosomal internal transcribed spacer region from a total of 293 type specimens of Agaricomycotina (Basidiomycota, Fungi) were conducted. Although more than 50% of those specimens produced positive PCR bands, a total of 114 specimens from National Museum of Nature and Science (TNS) and 21 specimens from Field Museum of Natural History (F), respectively, produced sequences of low quality with no discern- able peaks. All of the 43 good sequences obtained from the specimens at TNS were demonstrated to be from apparent contamination. In contrast, out of the 16 good sequences obtained from the specimens at F, only 2 sequences were from apparent contamination and the remaining 14 were considered authentic. The oldest specimen from which authentic sequence has been obtained was from 1940, but the PCR and sequencing success rate from older specimens was general low. This study clearly demonstrates the need of immediate DNA extraction from type specimens. Alterna- tively, small pieces of type specimens should be preserved separately from the herbarium for future DNA studies. Key words : BLAST, herbarium, ITS, mushrooms, taxonomy, type specimens. Introduction Fungi in general have limited morphological characters and mushrooms with macroscopic fruit bodies are no exception. It has often been demonstrated that mushrooms with similar or indistinguishable fruit body morphology repre- sent phylogenetically distantly related taxa (e.g., Kasuya et al., 2012; Wilson et al., 2016). For this reason, DNA sequence data, especially from the type specimens, are essential to establish stable taxonomic system of mushrooms. It is generally appreciated that the nuclear ribosomal internal transcribed spacer (ITS) region is an official DNA barcode region for fungi (Schoch et al., 2012). Although the ITS sequences cannot discriminate some closely related species, especially among Ascomycota, the presence of “universal” primers and high suc- cess rate of PCR and sequencing make this region widely applicable to many studies, such as taxonomy and ecology (Dentinger et al., 2010; Nagy et al., 2011; Schoch et al., 2012). In contrast to the rapid accumulation of the ITS sequences in GenBank, the number of sequences from the type specimens is not increasing at the same rate. The study by Nagy et al. (2011) showed that a number of unidentifiable sequences from environmental sequencing proj- ects matched with the sequences from the type strains of Mortierella. Similarly, Brock et al. (2009) estimated that ca. 70% of taxonomic diversity at the fungal herbarium of Kew Gar- dens alone was not yet represented in GenBank. These studies clearly demonstrated the need of obtaining ITS sequences from the type speci-
Transcript
Bull. Natl. Mus. Nat. Sci., Ser. B, 43(2), pp. 33–44, May 22, 2017
DNA Extraction, PCR and Sequencing were largely Unsuccessful from the Type Specimens of Mushrooms but Some 50-year-old or Older
Specimens produced Authentic Sequences
Kentaro Hosaka
Department of Botany, National Museum of Nature and Science, Amakubo 4–1–1, Tsukuba, Ibaraki 305–0005, Japan
Abstract DNA extraction, PCR and sequencing of the nuclear ribosomal internal transcribed spacer region from a total of 293 type specimens of Agaricomycotina (Basidiomycota, Fungi) were conducted. Although more than 50% of those specimens produced positive PCR bands, a total of 114 specimens from National Museum of Nature and Science (TNS) and 21 specimens from Field Museum of Natural History (F), respectively, produced sequences of low quality with no discern-able peaks. All of the 43 good sequences obtained from the specimens at TNS were demonstrated to be from apparent contamination. In contrast, out of the 16 good sequences obtained from the specimens at F, only 2 sequences were from apparent contamination and the remaining 14 were considered authentic. The oldest specimen from which authentic sequence has been obtained was from 1940, but the PCR and sequencing success rate from older specimens was general low. This study clearly demonstrates the need of immediate DNA extraction from type specimens. Alterna-tively, small pieces of type specimens should be preserved separately from the herbarium for future DNA studies.
Key words : BLAST, herbarium, ITS, mushrooms, taxonomy, type specimens.
Introduction
Fungi in general have limited morphological characters and mushrooms with macroscopic fruit bodies are no exception. It has often been demonstrated that mushrooms with similar or indistinguishable fruit body morphology repre-sent phylogenetically distantly related taxa (e.g., Kasuya et al., 2012; Wilson et al., 2016). For this reason, DNA sequence data, especially from the type specimens, are essential to establish stable taxonomic system of mushrooms.
It is generally appreciated that the nuclear ribosomal internal transcribed spacer (ITS) region is an official DNA barcode region for fungi (Schoch et al., 2012). Although the ITS sequences cannot discriminate some closely related species, especially among Ascomycota,
the presence of “universal” primers and high suc-cess rate of PCR and sequencing make this region widely applicable to many studies, such as taxonomy and ecology (Dentinger et al., 2010; Nagy et al., 2011; Schoch et al., 2012).
In contrast to the rapid accumulation of the ITS sequences in GenBank, the number of sequences from the type specimens is not increasing at the same rate. The study by Nagy et al. (2011) showed that a number of unidentifiable sequences from environmental sequencing proj-ects matched with the sequences from the type strains of Mortierella. Similarly, Brock et al. (2009) estimated that ca. 70% of taxonomic diversity at the fungal herbarium of Kew Gar-dens alone was not yet represented in GenBank. These studies clearly demonstrated the need of obtaining ITS sequences from the type speci-
Kentaro Hosaka34
mens to appropriately link fungal names and DNA sequence data.
Molecular studies using the type specimens, however, face a number of challenges. In gen-eral, DNA in specimens degrades with time (Erkens et al., 2008; Willerslev and Cooper, 2005), but the majority of type specimens are “old”. In addition, storage conditions such as temperature, humidity, and type of fumigation all affect the quality of DNA (Willerslev and Coo-per, 2005). It has also been demonstrated that older specimens tend to be more contaminated by other fungi (Brock et al., 2009).
In this study, the type specimens of diverse groups of mushrooms housed at two different herbaria collected in different times (from 1880’s to 1990’s) were tested for assessing the DNA quality. All specimens were extracted for genomic DNA, PCR amplified using general primers of the ITS, and sequence data were obtained by direct sequencing of PCR products. The aforementioned challenges are further emphasized, and a potential solution for future studies is presented.
Materials and Methods
Type specimens used in this studyA total of 235 specimens housed at the fungal
herbarium, Department of Botany, National Museum of Nature and Science, Tsukuba, Japan (TNS), and a total of 58 specimens housed at the Field Museum of Natural History, Chicago, USA (F) were studied. All of them were dried speci-mens with various ages (collection years ranged from 1882–1992). Specimens collected more recently (within 20 years) were intentionally excluded from this study because one of the main purposes was to assess the DNA quality from old specimens.
All specimens belong to the subphylum Agari-comycotina (mushrooms) of various families and orders (Table 2, 3). Although the original speci-men labels all indicate they are type specimens (including holotype, isotype and paratype), the nomenclatural status could not be confirmed for
some specimens. For example, “Ganoderma spathulatum” (TNS-F-201590) was indicated on the specimen label as “Typus” but no such names could be found either from Index Fungorum (http://www.indexfungorum.org/) or a cumula-tive list of Japanese fungi by Katsumoto (2010). Such species of uncertain type status are indi-cated with quotation marks throughout the text and tables (Table 2, 3).
All dried specimens, including the specimen labels and packets, were photographed for later assessing the quality of specimens, such as pres-ence of fungal or insect damage. Some represen-tative photographs and specimen data of type specimens were uploaded at Type Specimen Database of National Museum of Nature and Sci-ence, and they are publicly available from http://www.type.kahaku.go.jp/TypeDB/.
DNA preparation, PCR, sequencing, and BLAST search
DNA was extracted from hymenial tissues of dried specimens (~200 mg) stored overnight in DMSO buffer (Seutin et al., 1991; Hosaka, 2009). Tissues were first ground under liquid nitrogen using a mortar and pestle. Ground tis-sues were then transferred to new 1.5 ml tubes using clean spatulas, and CTAB buffer was added. DNA was extracted using the modified CTAB extraction protocol (Doyle and Doyle, 1987) followed by glass milk purification meth-ods as summarized by Hosaka (2009) and Hosaka and Castellano (2008). Briefly, ground samples were incubated in CTAB buffer at 65°C for 1 hour, and proteins were removed using the mixture of chloroform: isoamylalcohol (24 : 1). The materials were further purified using 6M sodium iodine buffer with glass milk, washed with ethanol/buffer solution, and finally eluted in 100 μl of TE buffer. All samples of extracted genomic DNA were deposited in the molecular laboratory, Department of Botany, National Museum of Nature and Science, Tsukuba, Japan, under the DNA voucher numbers denoted in Tables 2 and 3.
DNA sequence data were obtained from the
DNA from Type Specimens 35
ITS region using the primers ITS5 and ITS4 for amplifying ca. 600 bp region (White et al., 1990). PCR reactions were carried out using 20 μl reac-tion volumes each containing: 1 μl genomic DNA, 1 μl dNTPs (4 mM), 1 μl of each primer (8 μM), 0.5 units of Taq polymerase (TaKaRa, Tokyo, Japan), 2 μl MgCl2 (25 mM), 2 μl Bovine Serum Albumin (BSA). Cycling parameters were 1 cycle of 94°C for 3 min, 30 cycles of 94°C for 1 min, 51°C for 30 s and 72°C for 1 min, with a final extension at 72°C for 15 min. PCR products were electrophoresed in 1% agarose gels stained with ethidium bromide and visual-ized under UV light. When amplification bands were confirmed, the results were scored either as “successful (O)” (with single, clear band) or “failed (X)” (no bands or only smears were observed) (Tables 2, 3). PCR products were then purified using the ExoSap-IT (Millipore, Mol-sheim, France) and directly sequenced using the Big Dye Terminator Cycle Sequencing Kit on ABI3500 (Applied Biosystems Inc., Foster City, CA, USA), following the manufacturer’s instruc-tions.
Before editing raw sequence data, quality of sequences were scored as “good (O)” (readily editable sequences with clear chromatograms), “hetero (H)” (chromatograms with hetero-peaks), or “messy (X)” (sequences that are not editable with no discernable peaks), using Sequence Scanner version 1.0 (Applied Biosystems Inc., Foster City, CA, USA) (Table 2, 3). Only the sequences scored as “good” were further edited using ATGC version 7.1.0 (GENETYX Corpora-tion, Tokyo, Japan).
Edited sequences were analyzed using the GenBank BLAST search (Altschul et al., 1990). Default settings of blastn option were used such as “Database”＝“Others (nr etc.)” and “Program Selection”＝“Highly similar sequences (mega-blast)”. No parameters, such as “Max target sequences” and “Expect threshold”, were changed from the default settings. The top hit (regardless of its taxonomic level) and the next fully identified hit (to species level) were recorded. When those hits could be considered
erroneous (e.g., the top hit was ascomycetes but all the other hits showed basidiomycetous taxa), the “erroneous” hits were discarded and the results of the remaining hits were recorded.
Because sequence data from the majority of species tested in this study were expected not to be in GenBank database yet, BLAST results matched at generic level (or synonym of such) were considered “authentic” (DNA sequences were truly obtained from the specimens, not from the other sources). All the other matches were considered sequences from “apparent contamina-tion” (Table 1, 2, 3).
Results and Discussion
Most specimens used in this study were in “good” condition macroscopically, without obvi-ous insect damage (Fig. 1). However, some spec-imens had obvious fungal growth on the surface of fruit bodies, presumably by ascomycetous molds (Fig. 1A, D). The results of BLAST search indicated that sequences obtained from more than 20 specimens at TNS herbarium were from apparent contamination of ascomycetes (Table 1, 2). The visible presence of molds on fruit bodies was, however, not necessarily corresponding to the BLAST results. For example, “molds” on “Ganoderma spathulatum” (Fig. 1A) and Gas-
Table 1. Comparison of the results of PCR and sequencing from the specimens housed at two herbaria
Sequences with low quality 114 21Sequences with hetero-peaks 12 5Sequences from apparent
contamination43 2
Authentic sequences 0 14
*1 Department of Botany, National Museum of Nature and Science, Tsukuba, Japan.
*2 Department of Botany, Field Museum of Natural His-tory, Chicago, USA.
Kentaro Hosaka36
Table 2. Type specimens tested for this study housed at National Museum of Nature and Science (TNS) with the results of PCR and sequencing
Herbarium Voucher Nos.
DNA VoucherNos.*1
Order FamilyTaxon names in
the original label*2
Year collected
PCR*3 Sequencing*4 BLAST results*5
TNS-F-201590 A3016 Polyporales Ganodermataceae “Ganoderma spathulatum” 1891 X – –TNS-F-180124 A3056 Boletales Boletaceae Boletus hiratsukae 1896 O H –TNS-F-201999 A3023 Thelephorales Thelephoraceae Thelephora komabensis 1898 O X –TNS-F-206977 A3057 Polyporales Ganodermataceae Ganoderma subumbraculum 1908 O X –TNS-F-202252 A3025 Polyporales Polyporaceae Daedalea kusanoi 1909 O X –TNS-F-202482 A3001 Polyporales Polyporaceae Fomes olivaceus 1911 X – –TNS-F-202550 A3037 Polyporales Polyporaceae Fomes angularis 1912 O H –TNS-F-202243 A3061 Polyporales Polyporaceae Daedalea dickinsii 1912 O X –TNS-F-201565 A3006 Polyporales Polyporaceae Polyporus pubertatis 1912 X – –TNS-F-201364 A3031 Polyporales Polyporaceae Polyporus sendaiensis 1913 O H –TNS-F-202551 A3033 Polyporales Polyporaceae Fomes pusillus 1913 X – –TNS-F-203004 A2336 Russulales Stereaceae Stereum roseum 1913 X – –TNS-F-202818 A3028 Thelephorales Thelephoraceae Thelephora papillosa 1914 O H –TNS-F-202337 A3026 Polyporales Meruliaceae Merulius castaneus 1914 X – –TNS-F-201423 A2998 Polyporales Polyporaceae Polyporus versisporus 1914 X – –TNS-F-202805 A3027 Hymenochaetales Hymenochaetaceae Hymenochaete boninensis 1915 O H –TNS-F-203033 A3040 Russulales Stereaceae Stereum japonicum 1915 O H –TNS-F-201758 A3002 Polyporales Polyporaceae Polystictus nipponicus 1915 O X –TNS-F-201801 A3000 Polyporales Polyporaceae Polystictus glabratus 1915 O X –TNS-F-202823 A3034 Thelephorales Thelephoraceae Thelephora japonica 1915 O X –TNS-F-203077 A3029 Polyporales Meruliaceae Irpex iyoensis 1916 O H –TNS-F-203063 A3035 Polyporales Meruliaceae Irpex purpureus 1916 O X –TNS-F-202071 A3011 Polyporales Polyporaceae Trametes sensitivus 1916 O X –TNS-F-202757 A3067 Russulales Stereaceae Aleurodiscus japonicus 1916 O X –TNS-F-203006 A3007 Russulales Stereaceae Stereum sendaiense 1916 O X –TNS-F-203069 A2271 Polyporales Meruliaceae Irpex tabacinoides 1916 X – –TNS-F-202783 A3017 Russulales Stereaceae Stereum liratum 1916 X – –TNS-F-201575 A3032 Polyporales Ganodermataceae Ganoderma tsunodae 1917 O H –TNS-F-201448 A3036 Polyporales Polyporaceae Polyporus profissilis 1917 O H –TNS-F-207812 A3018 Agaricales Pterulaceae Pterula fusispora 1917 O X –TNS-F-202077 A3060 Polyporales Polyporaceae Trametes japonica 1917 O O uncultured ascomycetesTNS-F-195151 A2215 Cantharellales Cantharellaceae Cantharellus pallidus 1917 X – –TNS-F-202751 A3063 Russulales Stereaceae Aleurodiscus orientalis 1918 O X –TNS-F-202075 A3059 Polyporales Polyporaceae Trametes symploci 1918 O O RhodosporidiumTNS-F-201771 A2218 Hymenochaetales Hymenochaetaceae Coltriciella pusilla 1918 X – –TNS-F-204262 A2272 Polyporales Meruliaceae Irpex tabacinoides 1918 X – –TNS-F-201309 A2995 Polyporales Polyporaceae Polyporus greenii 1918 X – –TNS-F-201566 A3012 Polyporales Polyporaceae Polyporus kanehirae 1918 X – –TNS-F-202941 A3070 Russulales Stereaceae Coniophora matsuzawae 1918 X – –TNS-F-202748 A3062 Russulales Stereaceae Aleurodiscus tsugae 1919 O X –TNS-F-202774 A3069 Russulales Stereaceae “Aleurodiscus suborientalis” 1919 O X –TNS-F-202073 A3024 Polyporales Polyporaceae Trametes minutissima 1920 O X –TNS-F-202754 A3064 Russulales Stereaceae Aleurodiscus reflexus 1920 O X –TNS-F-202755 A3065 Russulales Stereaceae Aleurodiscus sendaiensis 1920 O X –TNS-F-202756 A3066 Russulales Stereaceae Aleurodiscus stereoides 1920 O X –TNS-F-201365 A2996 Polyporales Polyporaceae Polyporus sendaiensis 1921 O X –TNS-F-201366 A2997 Polyporales Polyporaceae Polyporus sendaiensis 1921 X – –TNS-F-203018 A3039 Russulales Stereaceae Stereum hamamelidis 1922 O H –TNS-F-203017 A3038 Russulales Stereaceae Stereum kurilense 1923 O H –TNS-F-201532 A3010 Polyporales Polyporaceae Polyporus liukiuensis 1923 O O PsathyrellaTNS-F-244375 A2179 Agaricales Strophariaceae Agrocybe media 1925 O X –TNS-F-201260 A3004 Polyporales Ganodermataceae Ganoderma hainanense 1928 O X –TNS-F-200234 A2261 Hymenochaetales Hymenochaetaceae Hymenochaete yasudai 1929 X – –TNS-F-200021 A3058 Polyporales Polyporaceae “Polyporus kinkazanensis” 1931 O X –TNS-F-203362 A3030 Hymenochaetales Hymenochaetaceae Hymenochaete rufo-marginata 1932 O H –TNS-F-200828 A2236 Polyporales Fomitopsidaceae “Fomitopsis laevigata” 1934 X – –TNS-F-200762 A3003 Polyporales Ganodermataceae Ganoderma neojaponicum 1935 O X –TNS-F-200900 A2306 Phallales Protophallaceae Protubera nipponica 1935 O O LaccariaTNS-F-172699 A3019 Agaricales Agaricaceae Cyathus badius 1936 O O PsathyrellaTNS-F-193009 A2197 Auriculariales Auriculariaceae Auricularia leucochroma 1936 X – –TNS-F-203372 A3021 Polyporales Polyporaceae Fomes mangrovicus 1937 X – –TNS-F-206958 A3005 Polyporales Polyporaceae Daedaleopsis nipponica 1938 O O PsathyrellaTNS-F-206965 A3013 Hymenochaetales Hymenochaetaceae Inonotus sciurinus 1938 X – –TNS-F-208290 A2278 Polyporales Polyporaceae Lentinus palauensis 1939 O X –TNS-F-207357 A3071 Hymenochaetales Hymenochaetaceae Hymenochaete yasudai 1939 O O PleurotusTNS-F-207357 A2262 Hymenochaetales Hymenochaetaceae Hymenochaete yasudai 1939 X – –TNS-F-190105 A2200 Auriculariales Auriculariaceae Auricularia semipellucida 1940 O X –TNS-F-208513 A2294 Agaricales Marasmiaceae Marasmius aurantiacus 1941 O X –TNS-F-6563 A2199 Auriculariales Auriculariaceae Auricularia polytricha 1941 X – –
DNA from Type Specimens 37
Herbarium Voucher Nos.
DNA VoucherNos.*1
Order FamilyTaxon names in
the original label*2
Year collected
PCR*3 Sequencing*4 BLAST results*5
TNS-F-212095 A3014 Hymenochaetales Hymenochaetaceae Cryptoderma cercidiphyllum 1941 X – –TNS-F-213570 A2237 Polyporales Fomitopsidaceae “Fomitopsis tenuis” 1943 O O uncultured ascomycetesTNS-F-237517 A2414 Russulales Russulaceae Russula kansaiensis 1945 O X –TNS-F-237667 A2318 Agaricales Entolomataceae Rhodophyllus cyanoniger 1950 O X –TNS-F-234247 A2217 Agaricales Omphalotaceae Collybia ozeensis 1950 X – –TNS-F-237485 A2303 Agaricales Pleurotaceae Pleurotus incarnatus 1952 O X –TNS-F-237560 A2339 Agaricales Strophariaceae Stropharia rugosoannulata 1952 O X –TNS-F-237621 A2344 Agaricales Tricholomataceae Tricholoma muscarium 1952 O X –TNS-F-237369 A2284 Agaricales Agaricaceae Lepiota clypeolaria 1953 O X –TNS-F-237379 A2291 Agaricales Lyophyllaceae Lyophyllum musashiense 1953 O X –TNS-F-237296 A2216 Agaricales Omphalotaceae Collybia neofusipes 1953 X – –TNS-F-237333 A2257 Agaricales Hygrophoraceae Hygrophorus pseudococcineus 1954 O X –TNS-F-237490 A2309 Agaricales Tricholomataceae Pseudohiatula ohshimae 1954 O X –TNS-F-237518 A2329 Russulales Russulaceae Russula metachroa 1954 O X –TNS-F-237522 A2332 Russulales Russulaceae Russula niigatensis 1954 O X –TNS-F-237523 A2333 Russulales Russulaceae Russula omiensis 1954 O X –TNS-F-237524 A2334 Russulales Russulaceae Russula subnigricans 1954 O X –TNS-F-237307 A2229 Agaricales Cortinariaceae Cortinarius subalboviolaceus 1954 O O uncultured ascomycetesTNS-F-237325 A2249 Agaricales Hygrophoraceae Hygrophorus dichrous 1954 O O uncultured ascomycetesTNS-F-237319 A2244 Boletales Hygrophoropsidaceae Hygrophoropsis bicolor 1954 O O uncultured ascomycetesTNS-F-237304 A2223 Agaricales Cortinariaceae Cortinarius claricolor 1954 X – –TNS-F-237328 A2252 Agaricales Hygrophoraceae Hygrophorus imazekii 1954 X – –TNS-F-237347 A2263 Agaricales Inocybaceae Inocybe ammophila 1954 X – –TNS-F-237373 A2286 Agaricales Agaricaceae Lepiota subcitrophylla 1955 O X –TNS-F-237480 A2297 Agaricales Mycenaceae Mycena umbilicata 1955 O X –TNS-F-237491 A2311 Agaricales Hymenogastraceae Psilocybe fasciata 1955 O X –TNS-F-237519 A2330 Russulales Russulaceae Russula nauseosa 1955 O X –TNS-F-237375 A2287 Agaricales Agaricaceae Leucocoprinus denudatus 1955 O O LaccariaTNS-F-237273 A2178 Agaricales Bolbitiaceae Agrocybe farinacea 1956 O X –TNS-F-237278 A2186 Agaricales Amanitaceae Amanita lutescens 1956 O X –TNS-F-237276 A2183 Agaricales Amanitaceae Amanita citrina 1956 O X –TNS-F-237281 A2189 Agaricales Amanitaceae Amanita pseudoporphyria 1956 O X –TNS-F-237479 A2296 Agaricales Mycenaceae Mycena roseomarginata 1956 O X –TNS-F-237619 A2343 Agaricales Tricholomataceae Tricholoma maculatipus 1956 O X –TNS-F-237359 A2275 Russulales Russulaceae Lactarius circellatus 1956 O X –TNS-F-237229 A2228 Agaricales Cortinariaceae Cortinarius shigaensis 1956 O O uncultured ascomycetesTNS-F-237321 A2245 Agaricales Hygrophoraceae Hygrophorus cantharellus 1956 O O uncultured ascomycetesTNS-F-237385 A2288 Agaricales Agaricaceae Leucocoprinus otsuensis 1956 O O LaccariaTNS-F-237494 A2316 Agaricales Entolomataceae Rhodophyllus ater 1956 O O uncultured ascomycetesTNS-F-237301 A2220 Agaricales Cortinariaceae Cortinarius aurantiofulvus 1956 X – –TNS-F-237284 A2201 Agaricales Bolbitiaceae Bolbitius incarnatus 1957 O X –TNS-F-237367 A2282 Agaricales Agaricaceae Lepiota aurantioflava 1957 O X –TNS-F-237625 A2345 Agaricales Tricholomataceae Tricholomopsis bambusina 1957 O X –TNS-F-237309 A2231 Agaricales Cortinariaceae Cortinarius subdelibutus 1957 O O uncultured ascomycetesTNS-F-237324 A2248 Agaricales Hygrophoraceae Hygrophorus cruentus 1957 O O uncultured ascomycetesTNS-F-237352 A2267 Agaricales Inocybaceae Inocybe macrosperma 1957 O O uncultured ascomycetesTNS-F-237492 A2312 Agaricales Hymenogastraceae Psilocybe subcaerulipes 1957 O O LaccariaTNS-F-237332 A2256 Agaricales Hygrophoraceae Hygrophorus pantoleucus 1957 X – –TNS-F-237351 A2266 Agaricales Inocybaceae Inocybe kobayasii 1957 X – –TNS-F-237365 A2280 Agaricales Agaricaceae Lepiota alborubescens 1958 O X –TNS-F-237368 A2283 Agaricales Agaricaceae Lepiota cinnamomea 1958 O X –TNS-F-237495 A2317 Agaricales Entolomataceae Rhodophyllus babingtonii 1958 O X –TNS-F-237629 A2347 Agaricales Tricholomataceae Tricholomopsis sasae 1958 O X –TNS-F-237322 A2246 Agaricales Hygrophoraceae Hygrophorus conicus 1958 O O uncultured ascomycetesTNS-F-237366 A2281 Agaricales Agaricaceae Lepiota atrosquamulosa 1958 O O LaccariaTNS-F-237487 A2305 Boletales Boletaceae Porphyrellus subvirens 1958 O O LaccariaTNS-F-237337 A2259 Agaricales Hygrophoraceae Hygrophorus subcinnabarinus 1958 X – –TNS-F-237354 A2269 Agaricales Inocybaceae Inocybe subvolvata 1958 X – –TNS-F-237277 A2184 Agaricales Amanitaceae Amanita griseofarinosa 1959 O X –TNS-F-237508 A2323 Agaricales Entolomataceae Rhodophyllus omiensis 1960 O X –TNS-F-237303 A2222 Agaricales Cortinariaceae Cortinarius cinnamomeoides 1960 X – –TNS-F-237329 A2253 Agaricales Hygrophoraceae Hygrophorus lilacinogriseus 1960 X – –TNS-F-237645 A2270 Agaricales Inocybaceae Inocybe subvolvata 1960 X – –TNS-F-237647 A2349 Boletales Boletaceae Tylopilus areolatus 1961 O X –TNS-F-237641 A2361 Boletales Boletaceae Xerocomus nigromaculatus 1961 O X –TNS-F-237310 A2232 Agaricales Cortinariaceae Cortinarius watamukiensis 1961 O O uncultured ascomycetesTNS-F-237481 A2298 Agaricales Strophariaceae Naematoloma gracile 1961 O O LaccariaTNS-F-237338 A2260 Agaricales Hygrophoraceae Hygrophorus suzukaensis 1961 X – –TNS-F-237353 A2268 Agaricales Inocybaceae Inocybe quercina 1961 X – –TNS-F-237637 A2356 Boletales Boletaceae Tylopilus otsuensis 1962 O X –
Table 2. Continued
Kentaro Hosaka38
Herbarium Voucher Nos.
DNA VoucherNos.*1
Order FamilyTaxon names in
the original label*2
Year collected
PCR*3 Sequencing*4 BLAST results*5
TNS-F-237652 A2363 Boletales Boletaceae Xerocomus parvulus 1962 O X –TNS-F-237525 A2335 Russulales Russulaceae Russula virescens 1962 O X –TNS-F-193006 A2235 Agaricales Mycenaceae Dictyopanus orientalis 1962 O O uncultured ascomycetesTNS-F-174776 A2355 Boletales Boletaceae Tylopilus otsuensis 1962 O O LaccariaTNS-F-237350 A2265 Agaricales Inocybaceae Inocybe kasugayamensis 1962 X – –TNS-F-237362 A2276 Russulales Russulaceae Lactarius subpiperatus 1963 O X –TNS-F-237231 A2230 Agaricales Cortinariaceae Cortinarius subarmillatus 1963 O O uncultured ascomycetesTNS-F-237382 A2293 Agaricales Marasmiaceae Marasmius aurantioferrugineus 1963 O O RhodosporidiumTNS-F-237297 A2219 Agaricales Psathyrellaceae Coprinus aokii 1963 O – –TNS-F-237355 A2273 Agaricales Strophariaceae Kuehneromyces castaneus 1963 X – –TNS-F-237557 A2337 Agaricales Strophariaceae Stropharia aeruginosa 1964 O X –TNS-F-237558 A2338 Agaricales Strophariaceae Stropharia aeruginosa 1964 O X –TNS-F-174775 A2365 Boletales Boletaceae Xerocomus nigromaculatus 1964 O X –TNS-F-237228 A2224 Agaricales Cortinariaceae Cortinarius galeroides 1964 X – –TNS-F-244373 A2191 Agaricales Amanitaceae Amanita rufoferruginea 1965 O X –TNS-F-237348 A2264 Agaricales Inocybaceae Inocybe atroumbonata 1965 O X –TNS-F-237330 A2254 Agaricales Hygrophoraceae Hygrophorus olivaceoviridis 1965 X – –TNS-F-237489 A2308 Agaricales Bolbitiaceae Pseudoconocybe nodulosospora 1966 O X –TNS-F-174771 A2354 Boletales Boletaceae Tylopilus neofelleus 1966 O O LaccariaTNS-F-237305 A2225 Agaricales Cortinariaceae Cortinarius neoarmillatus 1966 X – –TNS-F-237331 A2255 Agaricales Hygrophoraceae Hygrophorus olivaceoviridis 1966 X – –TNS-F-237287 A2207 Boletales Boletaceae Boletus griseus 1966 X – –TNS-F-237288 A2209 Boletales Boletaceae Boletus laetissimus 1966 X – –TNS-F-237289 A2210 Boletales Boletaceae Boletus obscureumbrinus 1966 X – –TNS-F-244377 A2192 Agaricales Amanitaceae Amanita sphaerobulbosa 1967 O X –TNS-F-237510 A2326 Russulales Russulaceae Russula bella 1967 O O LaccariaTNS-F-237226 A2205 Agaricales Amanitaceae Amanita neoovoidea 1967 X – –TNS-F-237293 A2214 Boletales Boletaceae Boletus umbiriniporus 1967 X – –TNS-F-237655 A2213 Boletales Boletaceae Boletus subfuscus 1967 X – –TNS-F-237372 A2285 Agaricales Agaricaceae Lepiota neomastoidea 1968 O X –TNS-F-237504 A2320 Agaricales Entolomataceae Rhodophyllus kansaiensis 1968 O X –TNS-F-237651 A2348 Boletales Boletaceae Tylopilus alutaceoumbrinus 1968 O X –TNS-F-50254 A2315 Gomphales Gomphaceae Ramaria zippelii 1968 O X –TNS-F-237306 A2226 Agaricales Cortinariaceae Cortinarius nigrosquamosus 1968 O O uncultured ascomycetesTNS-F-237323 A2247 Agaricales Hygrophoraceae Hygrophorus croceoluteus 1968 O O uncultured ascomycetesTNS-F-237274 A2181 Agaricales Amanitaceae Amanita alboflavescens 1969 X – –TNS-F-237488 A2307 Agaricales Psathyrellaceae Psathyrella pennata 1969 O X –TNS-F-234519 A2196 Auriculariales Auriculariaceae Auricularia fibrillifera 1969 O X –TNS-F-172603 A2353 Boletales Boletaceae Tylopilus hongoi 1969 O X –TNS-F-237283 A2193 Agaricales Amanitaceae Amanita sychnopyramis 1970 O X –TNS-F-244379 A2208 Agaricales Amanitaceae Amanita pseudogemmata 1970 X – –TNS-F-237302 A2221 Agaricales Cortinariaceae Cortinarius aureobrunneus 1970 X – –TNS-F-237290 A2211 Boletales Boletaceae Boletus pseudocalopus 1970 X – –TNS-F-228004 A2194 Agaricales Physalacriaceae Armillariella fellea 1971 O X –TNS-F-237377 A2289 Agaricales Agaricaceae Leucocoprinus subglobisporus 1971 O X –TNS-F-228005 A2295 Agaricales Omphalotaceae Micromphale pacificum 1971 O X –TNS-F-228018 A2299 Agaricales Strophariaceae Naematoloma papuanum 1971 O X –TNS-F-176271 A2304 Agaricales Mycenaceae Poromycena rubra 1971 O X –TNS-F-228000 A2346 Agaricales Tricholomataceae Tricholomopsis elata 1971 O X –TNS-F-225511 A2195 Boletales Boletaceae Aureoboletus novoguineensis 1971 O X –TNS-F-228299 A2301 Boletales Boletaceae Boletus oksapminensis 1971 O X –TNS-F-228001 A2279 Polyporales Polyporaceae Lentinus papuanus 1971 O X –TNS-F-225521 A2274 Russulales Russulaceae Lactarius austrovolemus 1971 O X –TNS-F-228002 A2300 Polyporales Polyporaceae Panus verruciceps 1971 O O LaccariaTNS-F-225479 A2328 Russulales Russulaceae Russula eburneoareolata 1971 O O LaccariaTNS-F-237513 A2327 Russulales Russulaceae Russula castanopsidis 1971 O O LaccariaTNS-F-228066 A2241 Agaricales Strophariaceae Gymnopilus novoguineensis 1971 X – –TNS-F-225485 A2203 Boletales Boletaceae Boletus erythropus 1971 X – –TNS-F-237275 A2182 Agaricales Amanitaceae Amanita castanopsidis 1972 X – –TNS-F-237364 A2277 Boletales Boletaceae Leccinum subradicatum 1972 O O uncultured ascomycetesTNS-F-237503 A2319 Agaricales Entolomataceae Rhodophyllus kansaiensis 1973 O X –TNS-F-237313 A2234 Agaricales Agaricaceae Cystoderma neoamianthinum 1973 O O uncultured ascomycetesTNS-F-237314 A2238 Agaricales Hymenogastraceae Galerina fasciculata 1973 X – –TNS-F-182277 A2212 Boletales Boletaceae “Boletus subcinnamomeus” 1973 X – –TNS-F-228435 A2310 Agaricales Hymenogastraceae Psilocybe argentipes 1975 O X –TNS-F-174773 A2360 Boletales Boletaceae Tylopilus vinosobrunneus 1975 O X –TNS-F-237648 A2352 Boletales Boletaceae Tylopilus eximus 1975 O X –TNS-F-237285 A2206 Boletales Boletaceae Boletus fuscopunctatus 1975 X – –TNS-F-198224 A2187 Agaricales Amanitaceae Amanita miculifera 1976 O X –TNS-F-198225 A2188 Agaricales Amanitaceae Amanita miculifera 1976 O X –
Table 2. Continued
DNA from Type Specimens 39
troboletus doii (Fig. 1D) were not amplified (PCR amplification was negative for both cases). On the other hand, some specimens without visi-ble molds on the surface also resulted in “appar-ent contamination” (Table 1, 2) using BLAST. Many ascomycetous molds can secondarily colo-nize on mushroom specimens and old specimens have much higher risk of such contamination. When dealing with old specimens, visual inspec-tion of specimens by stereo microscope and PCR amplification using basidiomycetes specific primers can minimize the risk of contamination, but we always need to recognize that old speci-mens are always contaminated by other (micro-) organisms by certain extent.
Such “apparent contamination” was caused not only by ascomycetes, but also by other basidio-mycetous mushrooms. For example, the sequence obtained from Amanita aestivalis F-1099363 (Amanitaceae) matched with Pholi-ota (Strophariaceae) (Table 3). Similarly, the
sequence from Leccinum albellum F-1015573 (Boletales) matched with Skeletocutis (Polypora-les) (Table 3). It is noteworthy that the sequences from various TNS specimens matched with unre-lated mushroom Laccaria (Hydnangiaceae) (Table 2). During this study, the project on Lac-caria phylogeography was on-going at the same time, and a large number of Laccaria specimens were processed in the same molecular lab. I believe “apparent contamination” of Laccaria was partially caused by genomic DNA acciden-tally mixed in some reagents commonly used in our molecular lab. It should be emphasized that no such Laccaria contamination has been detected in any other studies conducted in our molecular lab ever since.
Although the contamination by ascomycetes tends to be more frequent, mushroom contamina-tion by other mushrooms is also widespread as shown here. Such contamination at molecular lab can be avoided by always using fresh reagents,
Herbarium Voucher Nos.
DNA VoucherNos.*1
Order FamilyTaxon names in
the original label*2
Year collected
PCR*3 Sequencing*4 BLAST results*5
TNS-F-237633 A2359 Boletales Boletaceae Tylopilus ruguloso-reticulatus 1976 O X –TNS-F-237326 A2250 Agaricales Hygrophoraceae Hygrophorus hahashimensis 1977 O X –TNS-F-237653 A2362 Boletales Boletaceae Xerocomus obscurebrunneus 1977 O X –TNS-F-237657 A2364 Boletales Boletaceae Xerocomus subcinnamomeus 1977 O X –TNS-F-237511 A2324 Russulales Russulaceae Russula alboareolata 1977 O X –TNS-F-237311 A2233 Agaricales Inocybaceae Crepidotus roseus 1977 O O uncultured ascomycetesTNS-F-237378 A2290 Agaricales Amanitaceae Limacella olivaceobrunnea 1977 O O LaccariaTNS-F-174748 A2258 Agaricales Hygrophoraceae Hygrophorus subacutus 1977 X – –TNS-F-237327 A2251 Agaricales Hygrophoraceae Hygrophorus hypohaemactus 1977 X – –TNS-F-237505 A2321 Agaricales Entolomataceae Rhodophyllus kujuensis 1978 O X –TNS-F-174772 A2358 Boletales Boletaceae Tylopilus ruguloso-reticulatus 1978 O X –TNS-F-174774 A2357 Boletales Boletaceae Tylopilus rigens 1978 O X –TNS-F-237520 A2331 Russulales Russulaceae Russula neoemetica 1978 O X –TNS-F-237512 A2325 Russulales Russulaceae Russula alboareolata 1978 O O LaccariaTNS-F-237282 A2190 Agaricales Amanitaceae Amanita pseudovaginata 1980 O X –TNS-F-237650 A2202 Boletales Boletaceae Boletus aokii 1980 X – –TNS-F-237646 A2350 Boletales Boletaceae Tylopilus argillaceus 1981 O X –TNS-F-182343 A2242 Agaricales Hymenogastraceae Hebeloma radicosoides 1983 O X –TNS-F-237654 A2351 Boletales Boletaceae Tylopilus castaneiceps 1983 O X –TNS-F-237506 A2322 Agaricales Entolomataceae Rhodophyllus kujuensis 1983 O O LaccariaTNS-F-237562 A2342 Agaricales Tricholomataceae Tricholoma aurantiipes 1985 O X –TNS-F-237381 A2292 Agaricales Lyophyllaceae Lyophyllum sykosporum 1986 O X –TNS-F-237316 A2243 Agaricales Hygrophoraceae Hygrocybe miniatoaurantiaca 1987 O O uncultured ascomycetesTNS-F-237670 A2180 Agaricales Hymenogastraceae Alnicola lactariolens 1988 O X –TNS-F-200842 A3009 Polyporales Polyporaceae Polyporus tuberaster 1992 O X –TNS-F-171953 A2240 Boletales Boletaceae Gastroboletus doii 1992 X – –
*1 DNA sampes are stored under the DNA voucher numbers at Department of Botany, National Museum of Nature and Science, Tsukuba, Japan.*2 Species names with uncertain nomenclatural status were indicated with quotation marks.*3 PCR amplification was condidered “successful” with clear single band (O) or “failed” with no bands or smears (X).*4 Direct sequencing resulted in clear, readily editable sequences was considered “good” (O). Sequences were considered low quality or “messy” with no
discernable peaks (X). Sequences with hetero-peaks are indicated with “H”. *5 The results of the top hit are shown.
Table 2. Continued
Kentaro Hosaka40
Table 3. Type specimens tested for this study housed at Field Museum of Natural History (F) with the results of PCR and sequencing
Herbarium Voucher Nos.
DNA VoucherNos.*1
Order FamilyTaxon names in
the original label*2
Year collected
PCR*3 Sequencing*4 BLAST results*5
F-1037060 A2771 Russulales Russulaceae Lactarius mamorensis 1882 O X –F-332202 A2768 Boletales Boletaceae Boletus debeauxii 1884 O X –F-1295888 A2785 Agaricales Agaricaceae Lepiota denudata 1892 X – –F-1174531 A2739 Agaricales Agaricaceae Lepiota naucinoides 1893 O X –F-1247332 A2760 Russulales Russulaceae Lactarius rubrifulvus 1904 X – –F-497510 A2795 Agaricales Amanitaceae Amanita protecta 1920 O X –F-1001353 A2777 Russulales Stereaceae Aleurodiscus scutellatus 1926 X – –F-1001210 A2764 Russulales Russulaceae Arcangeliella scissilis 1933 X – –F-1201600 A2737 Agaricales Agaricaceae Lepiota fischeri 1938 O X –F-1152706 A2784 Agaricales Agaricaceae Lepiota cystidiosa 1940 O O Cystolepiota cystidiosaF-1001332 A2736 Agaricales Marasmiaceae Lactocollybia angiospermarum 1942 O X –F-1330205 A2782 Agaricales Agaricaceae Lepiota aurora 1948 O X –F-1330212 A2790 Agaricales Amanitaceae Amanita tenuifolia 1948 O X –F-1099363 A2747 Agaricales Amanitaceae Amanita aestivalis 1953 O O PholiotaF-1020987 A2767 Boletales Boletaceae Boletus guadelupae 1957 O O Boletus erythropusF-1037071 A2772 Russulales Russulaceae Lactarius paulensis 1964 X – –F-1014447 A2786 Agaricales Agaricaceae Lepiota xanthophylloides 1966 X – –F-1016880 A2773 Agaricales Hydnangiaceae “Laccaria carbonophila” 1967 O O LaccariaF-1013501 A2794 Agaricales Hygrophoraceae Botrydina lobata 1968 O H –F-1015825 A2765 Boletales Boletaceae Boletus fuligineotomentosus 1968 O X –F-1018786 A2758 Agaricales Hydnangiaceae Laccaria laccata var. vulcanica 1968 O O LaccariaF-1080297 A2799 Boletales Boletaceae “Boletus ixoflavus” 1969 X – –F-1080296 A2803 Boletales Boletaceae Boletus subluridellus 1969 O H –F-1018284 A2734 Boletales Boletaceae Boletus michoacanus 1969 O X –F-1015573 A2759 Boletales Boletaceae Leccinum albellum 1969 O O SkeletocutisF-1016998 A2801 Agaricales Hydnangiaceae “Laccaria moelleri” 1970 O O LaccariaF-1017120 A2743 Agaricales Hydnangiaceae Laccaria pussilla 1970 O O LaccariaF-1015677 A2752 Agaricales Strophariaceae Agrocybe amara 1970 O O Agrocybe praecoxF-1016843 A2762 Agaricales Hydnangiaceae Laccaria montana 1971 X – –F-1018209 A2738 Agaricales Bolbitiaceae Bolbitius mesosporus 1973 X – –F-1019126 A2774 Agaricales Hydnangiaceae Laccaria laccata 1974 X – –F-1018595 A2778 Agaricales Hydnangiaceae Laccaria laccata var. pusilla 1974 O X –F-1021123 A2757 Agaricales Hydnangiaceae Laccaria laccata var. tatrensis 1974 O O LaccariaF-1030847 A2766 Agaricales Bolbitiaceae Boletellus sp. 1976 O X –F-1030894 A2791 Boletales Boletaceae Boletellus ananas var. crassotunicatus 1976 O X –F-1037055 A2749 Russulales Russulaceae Lactarius amazonensis 1977 O H –F-1097232 A2754 Boletales Boletaceae Boletellus ananas 1978 O X –F-1037054 A2761 Russulales Russulaceae Lactarius subpallidipes 1978 O X –F-1031387 A2742 Agaricales Physalacriaceae Armillariella viridiflava 1979 X – –F-1030749 A2770 Russulales Russulaceae Lactarius igapoensis 1980 O X –F-1059109 A2744 Agaricales Hydnangiaceae “Laccaria kauaiensis” 1981 X – –F-1036989 A2781 Polyporales Polyporaceae Lentinus prancei 1981 O H –F-1037041 A2792 Russulales Russulaceae Lactarius costaricensis 1981 O O Lactarius fumosusF-1052251 A2769 Russulales Russulaceae Lactarius guanacastensis 1982 X – –F-1052236 A2800 Boletales Boletaceae Boletellus ananas 1982 X – –F-1051926 A2793 Agaricales Hydnangiaceae Laccaria gomezii 1982 O O LaccariaF-1073280 A2740 Agaricales Amanitaceae Amanita flavoconia 1983 O X –F-1053721 A2796 Agaricales Amanitaceae Amanita nauseosa 1983 O X –F-1073299 A2763 Boletales Boletaceae Boletus heterodermus 1983 O X –F-1160662 A2751 Agaricales Amanitaceae Agaricus pleropus 1984 X – –F-1091979 A2735 Agaricales Hydnangiaceae Laccaria longipes 1984 O X –F-1315642 A2802 Agaricales Agaricaceae Agaricus yucatanensis 1985 O X –F-1068563 A2797 Agaricales Physalacriaceae Armillariella affinis 1986 O H –F-1074629 A2745 Boletales Boletaceae Leccinum andinum 1986 O O Boletus bicolorF-1075916 A2798 Boletales Paxillaceae Austrogaster marthae 1988 X – –F-1097223 A2787 Boletales Boletaceae Laccinum roseoscabrum 1988 O O Leccinum talamancaeF-1100021 A2741 Boletales Boletaceae “Boletus pini-oocarpae” 1991 O O Boletus subvelutipesF-1097225 A2746 Boletales Boletaceae Leccinum roseoscabrum 1991 O O Leccinum talamancae
*1 DNA sampes are stored under the DNA voucher numbers at Department of Botany, National Museum of Nature and Science, Tsukuba, Japan.*2 Species names with uncertain nomenclatural status were indicated with quotation marks.*3 PCR amplification was condidered “successful” with clear single band (O) or “failed” with no bands or smears (X).*4 Direct sequencing resulted in clear, readily editable sequences was considered “good” (O). Sequences were considered low quality or “messy” with no dis-
cernable peaks (X). Sequences with hetero-peaks are indicated with “H”. *5 The results of the top hit are shown.
DNA from Type Specimens 41
Fig. 1. Some representatives of the type specimens tested in this study. A. “Ganoderma spathulatum” (TNS-F-201590) from 1891. B. Boletus hiratsukae (TNS-F-180124) from 1896.
C. Cystoderma neoamianthinum (TNS-F-237313) from 1973. D. Gastroboletus doii (TNS-F-171953) from 1992. E. Lactarius mamorensis (F-1037060) from 1882. F. Lepiota denudata (F-1295888) from 1892. G. Lepi-ota cystidiosa (F-1152706) from 1940. H. Agrocybe amara (F-1015677) from 1970. Bars＝2.5 cm.
Kentaro Hosaka42
but the contamination in the herbarium (e.g., mushroom specimens covered with spores of other mushrooms) is usually unavoidable. Researchers attempting to obtain DNA from old mushroom specimens should always be careful when interpreting the sequence data.
PCR amplification from more than 50% of specimens housed at TNS and F herbaria was successful (Table 1, Fig. 2, 3). Some specimens of more than 50 year old also had positive amplifica-tion (Fig. 2, 3). Although all successfully obtained sequences from TNS specimens were demon-strated to be from “apparent contamination”, the majority of direct sequencing was unsuccessful
due to low quality (114) and hetero-peaks (12), which may contain authentic sequences (Table 1). Similarly, out of 42 PCR products obtained from F specimens, only 14 produced authentic sequences and the remaining ones (21 low qual-ity sequences and 5 hetero-peaks) may contain authentic sequences as well (Table 1). This study is an initial screening of old type specimens and the next obvious step is to use taxon-specific primers and/or to sequence by cloning.
It is well documented from the previous stud-ies that many specimens at TNS have very frag-mented DNA due to fumigation (Hosaka and Uno, 2013). Most specimens of 30 year old or older have been fumigated by methyl bromide and the average lengths of DNA fragments were demonstrated to be 150 bp. or shorter (Hosaka and Uno, 2013). More recently, TNS herbarium has been fumigated by sulphuryl fluoride, which is claimed not to affect DNA molecules (Kigawa et al., 2003; Whitten et al., 1999). Although some positive PCR products with “failed” sequencing may contain authentic sequences, the possibility of obtaining ca. 600 bp. sequences using the primers ITS5 and ITS4 (White et al., 1990) is apparently low. The clear contrast in success rate of obtaining authentic sequences between TNS (0) and F (14) herbaria indicates that the effect of fumigation is not trivial. Although no detailed records of fumigation at F herbarium are currently available, the results of this study indicate that major fungal herbaria in the USA and Japan may have different fumiga-tion history.
It is obvious that DNA in specimens degrades with time (Erkens et al., 2008; Willerslev and Cooper, 2005). The current study shows that no authentic sequences were obtained from the specimens collected in 1930’s or before (Fig. 4). The oldest specimen from which we could PCR amplify the ITS region (ca. 600 bp.) and success-fully sequence was from 1940 (Lepiota cystidi-osa F-1152706) (Table 3, Fig. 1G, 4). Although other factors such as humidity, temperature and fumigation also affect the quality of DNA (Will-erslev and Cooper, 2005), this study clearly dem-
Fig. 2. Success rate of PCR amplification from the specimens stored at TNS herbarium.
Fig. 3. Success rate of PCR amplification from the specimens stored at F herbarium.
DNA from Type Specimens 43
onstrates the need of immediate DNA extraction from historically/taxonomically important speci-mens, i.e., type specimens. Historical records of fumigation in major fungal herbaria should be investigated for higher success rate of PCR and sequencing from such specimens. Alternatively, as suggested by Hosaka and Uno (2013), small pieces of type specimens should be preserved in deep-freezer, organic solvent (Fukatsu, 1999) or DNA preservation buffer (Dawson et al., 1998; Laulier et al., 1995; Nagy, 2010) for future molecular studies.
For future studies, the protocol for each step of DNA extraction, PCR and sequencing need to be re-examined. For example, fragmented DNA molecules are known to less effectively bind to silica particles (glass milk), but the binding effi-ciency can be improved by lowering the pH of the binding buffer (GENECLEAN Kit®, MP Bio-medicals, Solon, OH, USA; protocol available from https://www.funakoshi.co.jp/data/data sheet/GEN/1001-200.pdf). The PCR efficiency can certainly be improved by designing taxon-spe-cific primers and targeting shorter regions of DNA. As noted above, some “failed” sequences
in this study may contain authentic sequences, which can be obtained by cloning.
As initially expected, an attempt to obtain sequence data from the type specimens, espe-cially from old specimens, faced a lot of chal-lenges. As long as the fungal nomenclature is based on the principle of typification, however, further attempts should be made to obtain “authentic” sequence data from most, if not all, type specimens. If no such attempts are success-ful or type specimens are apparently absent, epi-typification from more recently collected speci-mens accompanied with good sequence data should be conducted (Hyde and Zhang, 2008).
Acknowledgments
The author thanks Kunihiko Uno and Kyung-Ok Nam for assisting my molecular work. I also thank Dr. Robert Luecking and other herbarium staffs for facilitating the loan of the type speci-mens from Field Museum of Natural History. This study was financed in part by a JSPS Grant-in-Aid for Young Scientists (A) (no. 24680085) and JSPS Grant-in-Aid for Scientific Research (B) (no. 40414362).
References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403–410.
Brock, P. M., Döring, H. and Bidartondo, M. I. 2008. How to know unknown fungi: the role of a herbarium. New Phytologist 181: 719–724.
Dawson, M. N., Raskoff, K. A. and Jacobs, D. K. 1998. Field preservation of marine invertebrate tissue for DNA analyses. Molecular Marine Biology and Bio-technology 7: 145–152.
Dentinger, B. T. M., Margaritescu, S. and Moncalvo, J.-M. 2010. Rapid and reliable high-throughput meth-ods of DNA extraction for use in barcoding and molec-ular systematics of mushrooms. Molecular Ecology Resources 10: 628–633.
Doyle, J. J. and Doyle, J. L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phy-tochemistry Bulletin 19: 11–15.
Erkens, R. H. J., Cross, H., Maas, J. W., Hoenselaar, K. and Chatrou, L. W. 2008. Assessment of age and green-
Fig. 4. Success rate of direct sequencing from the specimens stored at F herbarium.
Sequencing reactions producing “authentic” sequences were scored as success, and all the other sequences (apparent contamination, het-ero-peaks, and “messy” sequences) were scored as failed.
Kentaro Hosaka44
ness of herbarium specimens as predictors for success-ful extraction and amplification of DNA. Blumea 53: 407–428.
Fukatsu, T. 1999. Acetone preservation: a practical tech-nique for molecular analysis. Molecular Ecology 8: 1935–1945.
Hosaka, K. 2009. Phylogeography of the genus Pisolithus revisited with some additional taxa from New Caledo-nia and Japan. Bulletin of the National Museum of Nature and Science, Series B 35: 151–167.
Hosaka, K. 2015. Successful PCR amplification of Bacte-ria from mushroom fruit bodies. Bulletin of the National Museum of Nature and Science, Series B 41: 1–7.
Hosaka, K. and Castellano, M. A. 2008. Molecular phylo-genetics of Geastrales with special emphasis on the position of Sclerogaster. Bulletin of the National Museum of Nature and Science, Series B 34: 161–173.
Hosaka, K. and Uno, K. 2013. Assessment of the DNA quality in mushroom specimens: a recovery of the whole ITS sequence from fragmented DNA of the type specimen. Bulletin of the National Museum of Nature and Science, Series B 39: 53–60.
Hyde, K. D. and Zhang, Y. 2008. Epitypification: should we epitypify? Journal of Zhejiang University Science B 9: 842–846.
Kasuya, T., Hosaka, K., Uno, K. and Kakishima, M. 2012. Phylogenetic placement of Geastrum melano-cephalum and polyphyly of Geastrum triplex. Mycosci-ence 53: 411–426.
Katsumoto, K. 2010. List of fungi recorded in Japan. The Kanto Branch of Mycological Society of Japan, Funabashi, Chiba, Japan.
Kigawa, R., Nochide, H., Kimura, H. and Miura, S. 2003. Effects of various fumigants, thermal methods and car-bon dioxide treatment on DNA extraction and amplifi-cation: a case study on freeze-dried mushroom and freeze-dried muscle specimens. Collection Forum 18: 74–89.
Laulier, M., Pradier, E., Bigot, Y. and Périquet, G. 1995.
An easy method for preserving nucleic acids in field samples for later molecular and genetic studies without refrigerating. Journal of Evolutionary Biology 8: 657–663.
Nagy, Z. T. 2010. A hands-on overview of tissue preserva-tion methods for molecular genetic analyses. Organ-isms Diversity & Evolution 10: 91–105.
Nagy, L. G., Petkovits, T., Kovács, G. M., Voigt, K., Vágvölgyi, C. and Papp, T. 2011. Where is the unseen fungal diversity hidden? A study of Mortierella reveals a large contribution of reference collections to the iden-tification of fungal environmental sequences. New Phy-tologist 191: 789–794.
Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., Levesque, C. A., Chen, W. and Fungal Barcoding Consortium. 2012. Nuclear ribosomal inter-nal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences of the United States of America 109: 6241–6246.
Seutin, G., White, B. N. and Boag, P. T. 1991. Preserva-tion of avian blood and tissue samples for DNA analy-ses. Canadian Journal of Zoology 69: 82–90.
White, T. J., Bruns, T., Lee, S. and Taylor, J. W. 1990. Amplification and direct sequencing of fungal ribo-somal RNA genes for phylogenetics. In: Innis, M. A., Gelfand, D. H., Sninsky, J. J. and White, T. J. (eds.), PCR protocols, pp. 315–322, Academic Press, New York.
Whitten, W. M., Williams, N. H. and Glover, K. V. 1999. Sulphuryl fluoride fumigation: effect on DNA extrac-tion and amplification from herbarium specimens. Taxon 48: 507–510.
Willerslev, E. and Cooper, A. 2005. Ancient DNA. Pro-ceedings of the Royal Society B 272: 3–16.
Wilson, A. W., Hosaka, K. and Mueller, G. M. 2016. Evo-lution of ectomycorrhizas as a driver of diversification and biogeographic patterns in the model mycorrhizal mushroom genus Laccaria. New Phytologist 213: 1862–1873.
